Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments

After a limited first wave of community transmission in March 2020 and until 2022, Western Australia was largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite the low case load setting, sequencing of wastewater samples from large municipal treatment plants produced SARS-CoV-2 genomes with coverage up to 99.7 % and depth to 4000x, which was sufficient to link wastewater se-quences to those of active cases in the catchment at the time. This study demonstrates that <= 5 positive individuals can be enough to produce high genomic coverage (>90 %) assemblies even in catchments of up to a quarter of a million people. Genomic analysis of wastewater contemporaneous with clinical cases can also be used to rule out transmission between cases in different catchments, when their SARS-CoV-2 genomes have distinguishing nucleotide polymor-phisms. These findings reveal a greater potential of wastewater WGS to inform outbreak management and disease sur-veillance than previously recognized.

Automated summary

Western Australia was mostly free of COVID-19 from March 2020 to 2022, with limited community transmission. However, genomic analysis of wastewater samples showed that even a small number of positive individuals could be used to identify the source of active cases and rule out transmission between different catchments.